Complete genome sequence of the potato pathogen Ralstonia solanacearum UY031

Ralstonia solanacearum is the causative agent of bacterial wilt of potato. Ralstonia solanacearum strain UY031 belongs to the American phylotype IIB, sequevar 1, also classified as race 3 biovar 2. Here we report the completely sequenced genome of this strain, the first complete genome for phylotype IIB, sequevar 1, and the fourth for the R. solanacearum species complex. In addition to standard genome annotation, we have carried out a curated annotation of type III effector genes, an important pathogenicity-related class of genes for this organism. We identified 60 effector genes, and observed that this effector repertoire is distinct when compared to those from other phylotype IIB strains. Eleven of the effectors appear to be nonfunctional due to disruptive mutations. We also report a methylome analysis of this genome, the first for a R. solanacearum strain. This analysis helped us note the presence of a toxin gene within a region of probable phage origin, raising the hypothesis that this gene may play a role in this strain’s virulence.

• Publication year

  2016

• Venue

  Standards in Genomic Sciences

• Publication date

  2016-01-15

• Fields of study

  Biology, Medicine, Environmental Science

• Identifiers
  DOI 10.1186/s40793-016-0131-4PMID 26779304PMCID 4714475
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• List of new names and new combinations previously effectively, but not validly, published.

  2016cited by this paper
• Betaproteobacteria class. nov.

  2015cited by this paper
• DNA methylation in bacteria: from the methyl group to the methylome.

  2015cited by this paper
• Draft Genome Sequences of Ralstonia solanacearum Race 3 Biovar 2 Strains with Different Temperature Adaptations

  2015cited by this paper
• Burkholderiaceae fam. nov.

  2015cited by this paper
• Burkholderiales ord. nov

  2015cited by this paper
• REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

  2014cited by this paper
• Prokka: rapid prokaryotic genome annotation

  2014cited by this paper
• Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

  2013cited by this paper
• GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis

  2013cited by this paper
• Repertoire, unified nomenclature and evolution of the Type III effector gene set in the Ralstonia solanacearum species complex

  2013cited by this paper
• Top 10 plant pathogenic bacteria in molecular plant pathology.

  2012cited by this paper
• Pathogenomics of the Ralstonia solanacearum species complex.

  2012cited by this paper
• Complete Genome Sequence of the Plant Pathogen Ralstonia solanacearum Strain Po82

  2011influential reference
• Genetic Diversity and Aggressiveness of Ralstonia solanacearum Strains Causing Bacterial Wilt of Potato in Uruguay.

  2011influential reference
• Gram-Negative Bacteria

  2010influential reference
• Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence

  2010cited by this paper
• New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0.

  2010cited by this paper
• Antagonistic Effects of Some Lactobacilli On Some Gram-Negative Bacteria

  2010cited by this paper
• Direct detection of DNA methylation during single-molecule, real-time sequencing

  2010cited by this paper
• Characterization of filamentous bacteriophage PE226 infecting Ralstonia solanacearum strains

  2010cited by this paper
• REBASE—a database for DNA restriction and modification: enzymes, genes and genomes

  2009cited by this paper
• Specific genes from the potato brown rot strains of Ralstonia solanacearum and their potential use for strain detection.

  2009influential reference
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• The minimum information about a genome sequence (MIGS) specification

  2008cited by this paper
• Validation List no. 117. List of new names and new combinations previously effectively, but not validly, published.

  2007cited by this paper
• List of new names and new combinations previously effectively, but not validly, published.

  2006cited by this paper
• Identification of open reading frames unique to a select agent: Ralstonia solanacearum race 3 biovar 2.

  2006influential reference
• How complex is the Ralstonia solanacearum species complex

  2005cited by this paper
• Class II. Betaproteobacteria class. nov.

  2005cited by this paper
• Bacterial wilt disease and the Ralstonia solanacearum species complex

  2005cited by this paper
• MUSCLE: multiple sequence alignment with high accuracy and high throughput.

  2004cited by this paper
• Introduction to Europe of Ralstonia solanacearum biovar 2, race 3 in Pelargonium zonale cuttings from Kenya.

  2004cited by this paper
• OrthoMCL: identification of ortholog groups for eukaryotic genomes.

  2003cited by this paper
• Genome sequence of the plant pathogen Ralstonia solanacearum

  2002influential reference
• Laboratory guide for identification of plant pathogenic bacteria Third Edition

  2001cited by this paper
• Zonula Occludens Toxin Structure-Function Analysis

  2001cited by this paper
• Zonula occludens toxin structurefunction analysis. Identification of the fragment biologically active on tight junctions and of the zonulin receptor binding domain

  2000cited by this paper
• Gene Ontology: tool for the unification of biology

  2000cited by this paper
• An essential role for DNA adenine methylation in bacterial virulence.

  1999cited by this paper
• DNA adenine methylase mutants of Salmonella typhimurium show defects in protein secretion, cell invasion, and M cell cytotoxicity.

  1999cited by this paper
• Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

  1997cited by this paper
• Validation of the publication of new names and new combinations previously effectively published outside the IJSB.

  1996cited by this paper
• Transfer of Two Burkholderia and An Alcaligenes Species to Ralstonia Gen. Nov.

  1995cited by this paper
• Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.

  1990influential reference
• BIOINFORMATICS APPLICATIONS NOTE

  year unknowncited by this paper

• Bacterial wilt resistance is correlated with rhizosphere bacterial communities in wild potato Solanum malmeanum

  2026cites this paper
• Identification, characterization and genetic diversity of Ralstonia pseudosolanacearum causing bacterial wilt of tomato in Himachal Pradesh, India

  2025cites this paper
• Molecular identification and management of Ralstonia pseudosolanacearum (Phylotype I) causing bacterial wilt of tomatoes using copper oxide nanoparticles in Himachal Pradesh, India

  2025cites this paper
• Pathogenic and Comparative Genomic Analysis of Ralstonia pseudosolanacearum Isolated from Casuarina.

  2024cites this paper
• Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification

  2022cites this paper
• Biotechnological Approaches to Increase the Bacterial and Fungal Disease Resistance in Potato

  2022cites this paper
• Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex

  2022cites this paper
• Genome-scale Solanum spp.-Ralstonia solanacearum interactome reveals candidate determinants for host specificity and environmental adaptation

  2022influential citation
• Complete genome sequence analysis of the peanut pathogen Ralstonia solanacearum strain Rs-P.362200

  2021cites this paper
• Dynamic expression of Ralstonia solanacearum virulence factors and metabolism-controlling genes during plant infection

  2021cites this paper
• Global diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex

  2021cites this paper
• Molecular Detection of Ralstonia solanacearum to Facilitate Breeding for Resistance to Bacterial Wilt in Potato.

  2021cites this paper
• Light modulates important physiological features of Ralstonia pseudosolanacearum during the colonization of tomato plants

  2021cites this paper
• Plant pathogenic bacterium can rapidly evolve tolerance to an antimicrobial plant allelochemical

  2021influential citation
• A Meta-analysis of the known Global Distribution and Host Range of the Ralstonia Species Complex

  2020cites this paper
• Impact of UV irradiation at full scale on bacterial communities in drinking water

  2020cites this paper
• Phylotype and sequevar determination and AFLP fingerprinting of Ralstonia solanacearum strains causing bacterial wilt of potato in southeastern Iran

  2020cites this paper
• Draft Genome Sequences of Ralstonia solanacearum Isolated from Banana and Tomato in the Philippines

  2019influential citation
• Detection of Ralstonia solanacearum phylotype II, race 2 causing Moko disease and validation of genetic resistance observed in the hybrid plantain FHIA-21

  2019cites this paper
• Cryptic inoviruses revealed as pervasive in bacteria and archaea across Earth’s biomes

  2019cites this paper
• Complete genome sequence of the sesame pathogen Ralstonia solanacearum strain SEPPX 05

  2018cites this paper
• Big Data Analytics in Ralstonia solanacearum Genomics

  2018cites this paper
• Control strategies and gene expression dynamics of the plant pathogen Ralstonia solanacearum = Estratègies de control i dinàmica d'expressió gènica en el fitopatogen Ralstonia solanacearum

  2018influential citation
• High genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes

  2018cites this paper
• Characterization of CRISPR-Cas systems in the Ralstonia solanacearum species complex.

  2018cites this paper
• Transcriptomes of Ralstonia solanacearum during Root Colonization of Solanum commersonii

  2017influential citation
• Comparative Analysis of Ralstonia solanacearum Methylomes

  2017cites this paper
• Genome Sequencing of Ralstonia solanacearum CQPS-1, a Phylotype I Strain Collected from a Highland Area with Continuous Cropping of Tobacco

  2017cites this paper
• Three Draft Genome Sequences of the Bacterial Plant Pathogen Ralstonia solanacearum, Isolated in Georgia

  2017cites this paper
• 1 Recovery Plan for Ralstonia solanacearum Race 3 Biovar 2 Causing

  2017cites this paper
• HpaB-Dependent Secretion of Type III Effectors in the Plant Pathogens Ralstonia solanacearum and Xanthomonas campestris pv. vesicatoria

  2017cites this paper
• Interspecific Potato Breeding Lines Display Differential Colonization Patterns and Induced Defense Responses after Ralstonia solanacearum Infection

  2017cites this paper
• Biologie des populations du complexe d'espèces Ralstonia solanacearum appliquée à l'épidémiologie de la bactériose vasculaire de la pomme de terre à Madagascar

  2016cites this paper